I created this manifest file, and I am trying to import my data into qiime2. But I keep getting this error message. My data is demultiplexed and single end. I previously uploaded my data using the same manifest file and command and did not encounter this problem. I don't know what is wrong, any help would be appreciated
There are a couple of things you could change to troubleshoot this problem.
I think the manifest file has to be formatted as follows:
| sample-id | absolute-filepath |
|---|---|
| auc-control-2 | C:/Users/ranam/skin-24-7/sequences/C2.effective.fastq |
| auc-control-3 | C:/Users/ranam/skin-24-7/sequences/C3.effective.fastq |
| auc-control-5 | C:/Users/ranam/skin-24-7/sequences/C5.effective.fastq |
| minya-control-51 | C:/Users/ranam/skin-24-7/sequences/C51.effective.fastq |
| minya-acne-1 | C:/Users/ranam/skin-24-7/sequences/A1.effective.fastq |
| minya-acne-2 | C:/Users/ranam/skin-24-7/sequences/A2.effective.fastq |
| minya-acne-3 | C:/Users/ranam/skin-24-7/sequences/A3.effective.fastq |
| minya-acne-6 | C:/Users/ranam/skin-24-7/sequences/A6.effective.fastq |
That is, having no quotation marks around the absolute file paths and since you are using a Windows OS, the file paths should use '/' instead of '' to show path to subsequent subfolders.
I hope that helps!
Hi @RanaAbdelaal,
What operating system are you running this on? The manifest was clearly made on Windows, but they should be in LINUX / UNIX / Mac OS X path formats which may look like:
/Users/rana/myproject/...
or
/home/rana/myproject/...
If you are using the Windows Sub-System (WSL) for Linux, you may want to move your files inside the WSL env and and then update to the WSL file paths using the information here, see the figure.
If you are on a normal LINUX machine then simply update the file paths from Windows to LINUX format.
For WSL, the absolute path should simply be:
/home/rana/...
Move the folder of sequences to a location within WSL, do not try to access them on your Desktop. Then run the command again pointing to the WSL path.
For example in WSL, in your home directory do:
mkdir myproject
cd myproject
Then run the following as per the link I shared:
explorer.exe .
This will open a microsoft explorer window to the WSL path. Drag and drop your sequence folders and files into that window (which goes to the WSL directory). You'll see that they'll end up in the WSL path:
/home/rana/myproject/skin-24-7/....
Then update your manifest to point to the path where you just moved the sequences to, which should now be within WSL.
Then you should be able to run:
qiime tools import ....
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I changed the path to this
$PWD/sequences/A1.effective.fastq
and it worked, thanks so much!
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